TY - JOUR AU - Schmid, E. F. AU - Smith, D. A. PY - 2005 DA - 2005// TI - Keynote review: is declining innovation in the pharmaceutical industry a myth? JO - Drug Discov Today VL - 10 UR - https://doi.org/10.1016/S1359-6446(05)03524-5 DO - 10.1016/S1359-6446(05)03524-5 ID - Schmid2005 ER - TY - JOUR AU - Swinney, D. C. AU - Anthony, J. PY - 2011 DA - 2011// TI - How were new medicines discovered? JO - Nat Rev Drug Discov VL - 10 UR - https://doi.org/10.1038/nrd3480 DO - 10.1038/nrd3480 ID - Swinney2011 ER - TY - JOUR AU - Maziasz, T. AU - Kadambi, V. J. AU - Silverman, L. AU - Fedyk, E. AU - Alden, C. L. PY - 2010 DA - 2010// TI - Predictive toxicology approaches for small molecule oncology drugs JO - Toxicol Pathol VL - 38 UR - https://doi.org/10.1177/0192623309356448 DO - 10.1177/0192623309356448 ID - Maziasz2010 ER - TY - JOUR AU - Wang, Y. AU - Xing, J. AU - Xu, Y. AU - Zhou, N. AU - Peng, J. AU - Xiong, Z. AU - Liu, X. AU - Luo, X. AU - Luo, C. AU - Chen, K. AU - Zheng, M. AU - Jiang, H. PY - 2015 DA - 2015// TI - In silico ADME/T modelling for rational drug design JO - Q Rev Biophys VL - 48 UR - https://doi.org/10.1017/S0033583515000190 DO - 10.1017/S0033583515000190 ID - Wang2015 ER - TY - JOUR AU - Vedani, A. AU - Smiesko, M. PY - 2009 DA - 2009// TI - In silico toxicology in drug discovery—concepts based on three-dimensional models JO - Altern Lab Anim ATLA VL - 37 ID - Vedani2009 ER - TY - BOOK PY - 1996 DA - 1996// TI - Lipophilicity in drug action and toxicology PB - VCH Publishers CY - Weinheim ID - ref6 ER - TY - JOUR AU - Giuliano, K. A. PY - 1995 DA - 1995// TI - Aqueous two-phase partitioning. Physical chemistry and bioanalytical applications JO - FEBS Lett VL - 98 UR - https://doi.org/10.1016/0014-5793(95)90055-1 DO - 10.1016/0014-5793(95)90055-1 ID - Giuliano1995 ER - TY - JOUR AU - Kubinyi, H. PY - 1976 DA - 1976// TI - Quantitative structure–activity relationships. 2. A mixed approach, based on Hansch and free-Wilson analysis JO - J Med Chem VL - 19 UR - https://doi.org/10.1021/jm00227a004 DO - 10.1021/jm00227a004 ID - Kubinyi1976 ER - TY - JOUR AU - Hansch, C. AU - Hoekman, D. AU - Leo, A. AU - Zhang, L. AU - Li, P. PY - 1995 DA - 1995// TI - The expanding role of quantitative structure–activity relationships (QSAR) in toxicology JO - Toxicol Lett VL - 79 UR - https://doi.org/10.1016/0378-4274(95)03356-P DO - 10.1016/0378-4274(95)03356-P ID - Hansch1995 ER - TY - JOUR AU - Todeschini, R. AU - Consonni, V. PY - 2000 DA - 2000// TI - Handbook of molecular descriptors JO - New York VL - 11 ID - Todeschini2000 ER - TY - BOOK AU - Sheppard, S. PY - 2001 DA - 2001// TI - Handbook of property estimation methods for chemicals, environmental and health sciences PB - Lewis Publishers/CRC Press LLC CY - Boca Raton, Florida ID - Sheppard2001 ER - TY - JOUR AU - Livingstone, D. J. PY - 1994 DA - 1994// TI - Computational techniques for the prediction of toxicity JO - Toxicol Vitro VL - 8 UR - https://doi.org/10.1016/0887-2333(94)90091-4 DO - 10.1016/0887-2333(94)90091-4 ID - Livingstone1994 ER - TY - STD TI - TOPKAT (TOxicity Prediction by Komputer Assisted Technology). http://accelrys.com/ UR - http://accelrys.com/ ID - ref13 ER - TY - STD TI - ADMET Predictor™ (Simulations Plus, Inc., USA). http://www.simulations-plus.com/ UR - http://www.simulations-plus.com/ ID - ref14 ER - TY - STD TI - ADME-Tox Prediction (Advanced Chemistry Development, Inc., Canada). http://www.acdlabs.com/ UR - http://www.acdlabs.com/ ID - ref15 ER - TY - STD TI - DEREK (Lhasa Limited). http://www.lhasalimited.org/ UR - http://www.lhasalimited.org/ ID - ref16 ER - TY - STD TI - Toxicity Estimation Software Tools (U.S. Environmental Protection Agency). http://www2.epa.gov/chemical-research/toxicity-estimation-software-tool-test UR - http://www2.epa.gov/chemical-research/toxicity-estimation-software-tool-test ID - ref17 ER - TY - JOUR AU - Mitchell, J. B. O. PY - 2014 DA - 2014// TI - Machine learning methods in chemoinformatics JO - Wiley Interdiscip Rev Comput Mol Sci VL - 4 UR - https://doi.org/10.1002/wcms.1183 DO - 10.1002/wcms.1183 ID - Mitchell2014 ER - TY - STD TI - Hansen K (2012) Novel machine learning methods for computational chemistry. PhD thesis, Technical University of Berlin, Berlin. https://depositonce.tu-berlin.de/bitstream/11303/3606/1/Dokument_30.pdf UR - https://depositonce.tu-berlin.de/bitstream/11303/3606/1/Dokument_30.pdf ID - ref19 ER - TY - JOUR AU - Lavecchia, A. PY - 2015 DA - 2015// TI - Machine-learning approaches in drug discovery: methods and applications JO - Drug Discov Today VL - 20 UR - https://doi.org/10.1016/j.drudis.2014.10.012 DO - 10.1016/j.drudis.2014.10.012 ID - Lavecchia2015 ER - TY - JOUR AU - Judson, R. AU - Elloumi, F. AU - Setzer, R. W. AU - Li, Z. AU - Shah, I. PY - 2008 DA - 2008// TI - A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model JO - BMC Bioinform VL - 9 UR - https://doi.org/10.1186/1471-2105-9-241 DO - 10.1186/1471-2105-9-241 ID - Judson2008 ER - TY - JOUR AU - Kurczab, R. AU - Smusz, S. AU - Bojarski, A. PY - 2011 DA - 2011// TI - Evaluation of different machine learning methods for ligand-based virtual screening JO - J Cheminform VL - 3 UR - https://doi.org/10.1186/1758-2946-3-S1-P41 DO - 10.1186/1758-2946-3-S1-P41 ID - Kurczab2011 ER - TY - JOUR AU - Webb, S. J. AU - Hanser, T. AU - Howlin, B. AU - Krause, P. AU - Vessey, J. D. PY - 2014 DA - 2014// TI - Feature combination networks for the interpretation of statistical machine learning models: application to Ames mutagenicity JO - J Cheminform VL - 6 UR - https://doi.org/10.1186/1758-2946-6-8 DO - 10.1186/1758-2946-6-8 ID - Webb2014 ER - TY - JOUR AU - Melville, J. L. AU - Burke, E. K. AU - Hirst, J. D. PY - 2009 DA - 2009// TI - Machine learning in virtual screening JO - Comb Chem High Throughput Screen VL - 12 UR - https://doi.org/10.2174/138620709788167980 DO - 10.2174/138620709788167980 ID - Melville2009 ER - TY - JOUR AU - Varnek, A. AU - Baskin, I. PY - 2012 DA - 2012// TI - Machine learning methods for property prediction in chemoinformatics: Quo Vadis? JO - J Chem Inf Model VL - 52 UR - https://doi.org/10.1021/ci200409x DO - 10.1021/ci200409x ID - Varnek2012 ER - TY - JOUR AU - Krewski, D. AU - Acosta, D. AU - Andersen, M. AU - Anderson, H. AU - Bailar, J. C. AU - Boekelheide, K. AU - Brent, R. AU - Charnley, G. AU - Cheung, V. G. AU - Green, S. AU - Kelsey, K. T. AU - Kerkvliet, N. I. AU - Li, A. A. AU - McCray, L. AU - Meyer, O. AU - Patterson, R. D. AU - Pennie, W. AU - Scala, R. A. AU - Solomon, G. M. AU - Stephens, M. AU - Yager, J. AU - Zeise, L. PY - 2010 DA - 2010// TI - Toxicity testing in the 21st century: a vision and a strategy JO - J Toxicol Environ Health B VL - 13 UR - https://doi.org/10.1080/10937404.2010.483176 DO - 10.1080/10937404.2010.483176 ID - Krewski2010 ER - TY - JOUR AU - Huang, R. AU - Xia, M. AU - Nguyen, D. AU - Zhao, T. AU - Sakamuru, S. PY - 2016 DA - 2016// TI - Tox21 challenge to build predictive models of nuclear receptor and stress response pathways as mediated by exposure to environmental chemicals and drugs JO - Front Environ Sci VL - 3 UR - https://doi.org/10.3389/fenvs.2015.00085 DO - 10.3389/fenvs.2015.00085 ID - Huang2016 ER - TY - JOUR AU - Drwal, M. N. AU - Siramshetty, V. B. AU - Banerjee, P. AU - Goede, A. AU - Preissner, R. AU - Dunkel, M. PY - 2015 DA - 2015// TI - Molecular similarity-based predictions of the Tox21 screening outcome JO - Front Environ Sci VL - 3 ID - Drwal2015 ER - TY - STD TI - Tox21 Data Challenge 2014. https://tripod.nih.gov/tox21/challenge/leaderboard.jsp UR - https://tripod.nih.gov/tox21/challenge/leaderboard.jsp ID - ref29 ER - TY - STD TI - MACCS Structural keys; Accelrys: San Diego, CA, 2011. http://accelrys.com/ UR - http://accelrys.com/ ID - ref30 ER - TY - JOUR AU - Rogers, D. AU - Hahn, M. PY - 2010 DA - 2010// TI - Extended-connectivity fingerprints JO - J Chem Inf Model VL - 50 UR - https://doi.org/10.1021/ci100050t DO - 10.1021/ci100050t ID - Rogers2010 ER - TY - STD TI - ToxPrint. https://toxprint.org/ UR - https://toxprint.org/ ID - ref32 ER - TY - JOUR AU - Ashby, J. AU - Tennant, R. W. PY - 1988 DA - 1988// TI - Chemical structure, Salmonella mutagenicity and extent of carcinogenicity as indicators of genotoxic carcinogenesis among 222 chemicals tested in rodents by the U.S. NCI/NTP JO - Mutat Res VL - 204 UR - https://doi.org/10.1016/0165-1218(88)90114-0 DO - 10.1016/0165-1218(88)90114-0 ID - Ashby1988 ER - TY - JOUR AU - Kroes, R. AU - Renwick, A. G. AU - Cheeseman, M. AU - Kleiner, J. AU - Mangelsdorf, I. AU - Piersma, A. AU - Schilter, B. AU - Schlatter, J. AU - Schothorst, F. AU - Vos, J. G. AU - Würtzen, G. PY - 2004 DA - 2004// TI - European branch of the International Life Sciences Institute: structure-based thresholds of toxicological concern (TTC): guidance for application to substances present at low levels in the diet JO - Food Chem Toxicol VL - 42 UR - https://doi.org/10.1016/j.fct.2003.08.006 DO - 10.1016/j.fct.2003.08.006 ID - Kroes2004 ER - TY - JOUR AU - Hall, L. H. AU - Kier, L. B. PY - 1995 DA - 1995// TI - Electrotopological state indices for atom types: a novel combination of electronic, topological, and valence state information JO - J Chem Inf Model VL - 35 UR - https://doi.org/10.1021/ci00028a014 DO - 10.1021/ci00028a014 ID - Hall1995 ER - TY - JOUR AU - Johnson, M. AU - Basak, S. AU - Maggiora, G. PY - 1988 DA - 1988// TI - A characterization of molecular similarity methods for property prediction JO - Math Comput Model VL - 11 UR - https://doi.org/10.1016/0895-7177(88)90569-9 DO - 10.1016/0895-7177(88)90569-9 ID - Johnson1988 ER - TY - JOUR AU - Maggiora, G. AU - Vogt, M. AU - Stumpfe, D. AU - Bajorath, J. PY - 2014 DA - 2014// TI - Molecular similarity in medicinal chemistry JO - J Med Chem VL - 57 UR - https://doi.org/10.1021/jm401411z DO - 10.1021/jm401411z ID - Maggiora2014 ER - TY - JOUR AU - Stefaniak, F. PY - 2015 DA - 2015// TI - Prediction of compounds activity in nuclear receptor signaling and stress pathway assays using machine learning algorithms and low-dimensional molecular descriptors JO - Front Environ Sci VL - 3 ID - Stefaniak2015 ER - TY - JOUR AU - Plewczynski, D. PY - 2009 DA - 2009// TI - BRAINSTORMING: consensus learning in practice JO - Front Neuroinform VL - 679 ID - Plewczynski2009 ER - TY - JOUR AU - Liu, J. AU - Mansouri, K. AU - Judson, R. S. AU - Martin, M. T. AU - Hong, H. AU - Chen, M. AU - Xu, X. AU - Thomas, R. S. AU - Shah, I. PY - 2015 DA - 2015// TI - Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure JO - Chem Res Toxicol VL - 28 UR - https://doi.org/10.1021/tx500501h DO - 10.1021/tx500501h ID - Liu2015 ER - TY - STD TI - Mayr A, Klambauer G, Unterthiner T, Hochreiter S (2016) DeepTox: toxicity prediction using deep learning. Front Environ Sci 3:80 ID - ref41 ER - TY - STD TI - RDKit: Open-Source Cheminformatics Software. http://www.rdkit.org UR - http://www.rdkit.org ID - ref42 ER - TY - BOOK AU - Berthold, M. R. AU - Cebron, N. AU - Dill, F. AU - Gabriel, T. R. AU - Kötter, T. AU - Meinl, T. AU - Ohl, P. AU - Sieb, C. AU - Kilian Thiel, B. W. PY - 2008 DA - 2008// TI - KNIME: the Konstanz information miner PB - Springer CY - Berlin ID - Berthold2008 ER - TY - STD TI - KNIME AG. https://www.knime.org/ UR - https://www.knime.org/ ID - ref44 ER - TY - STD TI - Molecular Networks GmbH. https://www.molecular-networks.com/ UR - https://www.molecular-networks.com/ ID - ref45 ER - TY - JOUR AU - Hert, J. AU - Willett, P. AU - Wilton, D. J. AU - Acklin, P. AU - Azzaoui, K. AU - Jacoby, E. AU - Schuffenhauer, A. PY - 2004 DA - 2004// TI - Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures JO - J Chem Inf Comput Sci VL - 44 UR - https://doi.org/10.1021/ci034231b DO - 10.1021/ci034231b ID - Hert2004 ER - TY - JOUR AU - Willett, P. PY - 2003 DA - 2003// TI - Similarity-based approaches to virtual screening JO - Biochem Soc Trans VL - 31 UR - https://doi.org/10.1042/bst0310603 DO - 10.1042/bst0310603 ID - Willett2003 ER - TY - STD TI - Schapire R, Machine learning algorithms for classification. http://www.cs.princeton.edu/~schapire/talks/picasso-minicourse.pdf. Accessed 1 Nov 2015 UR - http://www.cs.princeton.edu/~schapire/talks/picasso-minicourse.pdf ID - ref48 ER - TY - JOUR AU - Breiman, L. PY - 2001 DA - 2001// TI - Random Forests JO - Mach Learn VL - 45 UR - https://doi.org/10.1023/A:1010933404324 DO - 10.1023/A:1010933404324 ID - Breiman2001 ER - TY - JOUR AU - Specht, D. F. PY - 1990 DA - 1990// TI - Probabilistic neural networks JO - Neural Netw VL - 3 UR - https://doi.org/10.1016/0893-6080(90)90049-Q DO - 10.1016/0893-6080(90)90049-Q ID - Specht1990 ER - TY - JOUR AU - Clark, A. M. AU - Dole, K. AU - Coulon-Spektor, A. AU - McNutt, A. AU - Grass, G. AU - Freundlich, J. S. AU - Reynolds, R. C. AU - Ekins, S. PY - 2015 DA - 2015// TI - Open source Bayesian models. 1. Application to ADME/Tox and drug discovery datasets JO - J Chem Inf Model VL - 55 UR - https://doi.org/10.1021/acs.jcim.5b00143 DO - 10.1021/acs.jcim.5b00143 ID - Clark2015 ER - TY - JOUR AU - Helma, C. AU - Cramer, T. AU - Kramer, S. AU - Raedt, L. PY - 2004 DA - 2004// TI - Data mining and machine learning techniques for the identification of mutagenicity inducing substructures and structure activity relationships of noncongeneric compounds JO - J Chem Inf Comput Sci VL - 44 UR - https://doi.org/10.1021/ci034254q DO - 10.1021/ci034254q ID - Helma2004 ER - TY - JOUR AU - Zhang, C. AU - Cheng, F. AU - Sun, L. AU - Zhuang, S. AU - Li, W. AU - Liu, G. AU - Lee, P. W. AU - Tang, Y. PY - 2015 DA - 2015// TI - In silico prediction of chemical toxicity on avian species using chemical category approaches JO - Chemosphere VL - 122 UR - https://doi.org/10.1016/j.chemosphere.2014.12.001 DO - 10.1016/j.chemosphere.2014.12.001 ID - Zhang2015 ER - TY - JOUR AU - Berthold, M. R. AU - Diamond, J. PY - 1998 DA - 1998// TI - Constructive training of probabilistic neural networks JO - Neurocomputing VL - 19 UR - https://doi.org/10.1016/S0925-2312(97)00063-5 DO - 10.1016/S0925-2312(97)00063-5 ID - Berthold1998 ER - TY - STD TI - Cheung V, Cannons K, An introduction to probabilistic neural networks. http://www.wi.hs-wismar.de/~cleve/vorl/projects/dm/ss13/PNN/Quellen/CheungCannons_AnIntroductiontoPNNs.pdf. Accessed 15 Nov 2015 UR - http://www.wi.hs-wismar.de/~cleve/vorl/projects/dm/ss13/PNN/Quellen/CheungCannons_AnIntroductiontoPNNs.pdf ID - ref55 ER - TY - STD TI - The University of Reading Website: Probabilistic neural network (PNN), pp 1–9 ID - ref56 ER - TY - JOUR AU - Browne, M. PY - 2000 DA - 2000// TI - Cross-validation methods JO - J Math Psychol VL - 44 UR - https://doi.org/10.1006/jmps.1999.1279 DO - 10.1006/jmps.1999.1279 ID - Browne2000 ER - TY - JOUR AU - Erkel, A. R. AU - Pattynama, P. M. PY - 1998 DA - 1998// TI - Receiver operating characteristic (ROC) analysis: basic principles and applications in radiology JO - Eur J Radiol VL - 27 UR - https://doi.org/10.1016/S0720-048X(97)00157-5 DO - 10.1016/S0720-048X(97)00157-5 ID - Erkel1998 ER - TY - JOUR AU - Pepe, M. S. PY - 2000 DA - 2000// TI - Receiver operating characteristic methodology JO - J Am Stat Assoc VL - 95 UR - https://doi.org/10.1080/01621459.2000.10473930 DO - 10.1080/01621459.2000.10473930 ID - Pepe2000 ER - TY - JOUR AU - Bewick, V. AU - Cheek, L. AU - Ball, J. PY - 2004 DA - 2004// TI - Statistics review 13: receiver operating characteristic curves JO - Crit Care VL - 8 UR - https://doi.org/10.1186/cc3000 DO - 10.1186/cc3000 ID - Bewick2004 ER -